/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.aaproperties.profeat;
import org.biojava.nbio.aaproperties.profeat.convertor.*;
import org.biojava.nbio.core.sequence.ProteinSequence;
import java.util.HashMap;
import java.util.Map;
public class ProfeatPropertiesImpl implements IProfeatProperties{
@Override
public double getComposition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception {
Convertor convertor = getConvertor(attribute);
String convertedSequence = convertor.convert(sequence);
return (getTotalCount(convertedSequence, group) + 0.0) / convertedSequence.length();
}
private int getTotalCount(String convertedSeq, GROUPING group) throws Exception{
char g;
switch(group){
case GROUP1: g = Convertor.group1; break;
case GROUP2: g = Convertor.group2; break;
case GROUP3: g = Convertor.group3; break;
default: throw new Exception("Unhandled Case: " + group);
}
int total = 0;
for(char c:convertedSeq.toCharArray()){
if(c == g) total++;
}
return total;
}
@Override
public double getTransition(ProteinSequence sequence, ATTRIBUTE attribute, TRANSITION transition) throws Exception{
Convertor convertor = getConvertor(attribute);
String convertedSequence = convertor.convert(sequence);
char t1;
char t2;
switch(transition){
case BETWEEN_11: t1 = '1'; t2 = '1'; break;
case BETWEEN_22: t1 = '2'; t2 = '2'; break;
case BETWEEN_33: t1 = '3'; t2 = '3'; break;
case BETWEEN_12: t1 = '1'; t2 = '2'; break;
case BETWEEN_13: t1 = '1'; t2 = '3'; break;
case BETWEEN_23: t1 = '2'; t2 = '3'; break;
default: throw new Exception("Unhandled Case: " + transition);
}
int total = 0;
for(int i = 0; i < convertedSequence.length() - 1; i++){
char s1 = convertedSequence.charAt(i);
char s2 = convertedSequence.charAt(i + 1);
if((t1 == s1 && t2 == s2) || (t2 == s1 && t1 == s2)) total++;
}
return total / (convertedSequence.length() - 1.0);
}
@Override
public double getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group, DISTRIBUTION distribution) throws Exception{
Convertor convertor = getConvertor(attribute);
String convertedSequence = convertor.convert(sequence);
int totalCount = getTotalCount(convertedSequence, group);
int countIndex;
switch(distribution){
case FIRST: countIndex = 1; break;
case FIRST25: countIndex = totalCount * 25 / 100; break;
case FIRST50: countIndex = totalCount * 50 / 100; break;
case FIRST75: countIndex = totalCount * 75 / 100; break;
case ALL: countIndex = totalCount; break;
default: throw new Exception("Unhandled Case: " + distribution);
}
char g;
switch(group){
case GROUP1: g = Convertor.group1; break;
case GROUP2: g = Convertor.group2; break;
case GROUP3: g = Convertor.group3; break;
default: throw new Exception("Unhandled Case: " + group);
}
int currentCount = 0;
int dist = 0;
for(int x = 0; x < convertedSequence.length(); x++){
if(g == convertedSequence.charAt(x)){
currentCount++;
if(currentCount == countIndex){
dist = x+1;
break;
}
}
}
return (dist + 0.0) / convertedSequence.length();
}
private Convertor getConvertor(ATTRIBUTE attribute) throws Exception{
switch(attribute){
case HYDROPHOBICITY: return new Convert2Hydrophobicity();
case VOLUME: return new Convert2NormalizedVanDerWaalsVolume();
case POLARITY: return new Convert2Polarity();
case POLARIZABILITY: return new Convert2Polarizability();
case CHARGE: return new Convert2Charge();
case SECONDARYSTRUCTURE: return new Convert2SecondaryStructure();
case SOLVENTACCESSIBILITY: return new Convert2SolventAccessibility();
default: throw new Exception("Unknown attribute: " + attribute);
}
}
@Override
public Map<GROUPING, Double> getComposition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
Map<GROUPING, Double> grouping2Composition = new HashMap<GROUPING, Double>();
for(GROUPING group:GROUPING.values()) grouping2Composition.put(group, getComposition(sequence, attribute, group));
return grouping2Composition;
}
@Override
public Map<ATTRIBUTE, Map<GROUPING, Double>> getComposition(ProteinSequence sequence) throws Exception {
Map<ATTRIBUTE, Map<GROUPING, Double>> attribute2Grouping2Composition = new HashMap<ATTRIBUTE, Map<GROUPING, Double>>();
for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Grouping2Composition.put(attribute, getComposition(sequence, attribute));
return attribute2Grouping2Composition;
}
@Override
public Map<TRANSITION, Double> getTransition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
Map<TRANSITION, Double> transition2Double = new HashMap<TRANSITION, Double>();
for(TRANSITION transition:TRANSITION.values()) transition2Double.put(transition, getTransition(sequence, attribute, transition));
return transition2Double;
}
@Override
public Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(ProteinSequence sequence) throws Exception {
Map<ATTRIBUTE, Map<TRANSITION, Double>> attribute2Transition2Double = new HashMap<ATTRIBUTE, Map<TRANSITION, Double>>();
for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Transition2Double.put(attribute, getTransition(sequence, attribute));
return attribute2Transition2Double;
}
@Override
public Map<DISTRIBUTION, Double> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception {
Map<DISTRIBUTION, Double> distribution2Double = new HashMap<DISTRIBUTION, Double>();
for(DISTRIBUTION distribution:DISTRIBUTION.values())
distribution2Double.put(distribution, getDistributionPosition(sequence, attribute, group, distribution));
return distribution2Double;
}
@Override
public Map<GROUPING, Map<DISTRIBUTION, Double>> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
Map<GROUPING, Map<DISTRIBUTION, Double>> grouping2Distribution2Double = new HashMap<GROUPING, Map<DISTRIBUTION, Double>>();
for(GROUPING group:GROUPING.values())
grouping2Distribution2Double.put(group, getDistributionPosition(sequence, attribute, group));
return grouping2Distribution2Double;
}
@Override
public Map<ATTRIBUTE, Map<GROUPING, Map<DISTRIBUTION, Double>>> getDistributionPosition(ProteinSequence sequence) throws Exception {
Map<ATTRIBUTE, Map<GROUPING, Map<DISTRIBUTION, Double>>> attribute2Grouping2Distribution2Double =
new HashMap<ATTRIBUTE, Map<GROUPING, Map<DISTRIBUTION, Double>>>();
for(ATTRIBUTE attribute:ATTRIBUTE.values())
attribute2Grouping2Distribution2Double.put(attribute, getDistributionPosition(sequence, attribute));
return attribute2Grouping2Distribution2Double;
}
}